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Proteomics Analysis
Comprehensive analysis of mass spectrometry-based proteomics data from protein identification through quantification, differential expression, post-translational modifications, and systems-level interpretation.
When to Use This Skill
Triggers : User has proteomics MS output files, asks about protein abundance/expression, differential protein expression, PTM analysis, protein-RNA correlation, multi-omics integration involving proteomics, protein complex/interaction analysis, or proteomics biomarker discovery.
Core Capabilities
| Capability | Description |
|---|
| Data Import | MaxQuant, Spectronaut, DIA-NN, Proteome Discoverer, FragPipe outputs |
| Quality Control | Missing value analysis, intensity distributions, sample clustering |
| Normalization | Median, quantile, TMM, VSN normalization methods |
| Imputation | MinProb, KNN, QRILC for missing values |
| Differential Expression | Limma, DEP, MSstats for statistical testing |
| PTM Analysis | Phospho-site localization, PTM enrichment, kinase prediction |
| Protein-RNA Integration | Correlation analysis, translation efficiency |
| Pathway Enrichment | Over-representation and GSEA for protein sets |
| PPI Analysis | Protein complex detection, interaction networks via STRING/IntAct |
| Reporting | Comprehensive reports with volcano plots, heatmaps, pathway diagrams |
Workflow Overview
Input: MS Proteomics Data
|
Phase 1: Data Import & QC
Phase 2: Preprocessing (filter, impute, normalize)
Phase 3: Differential Expression Analysis
Phase 4: PTM Analysis (if applicable)
Phase 5: Functional Enrichment (GO, KEGG, Reactome)
Phase 6: Protein-Protein Interactions (STRING networks)
Phase 7: Multi-Omics Integration (optional, protein-RNA correlation)
Phase 8: Generate Report
See PHASE_DETAILS.md for detailed procedures per phase.
Integration with ToolUniverse
| Skill | Used For | Phase |
|---|
tooluniverse-gene-enrichment | Pathway enrichment | Phase 5 |
tooluniverse-protein-interactions | PPI networks | Phase 6 |
tooluniverse-rnaseq-deseq2 | RNA-seq for integration | Phase 7 |
tooluniverse-multi-omics-integration | Cross-omics analysis | Phase 7 |
tooluniverse-target-research |
Quantified Minimums
| Component | Requirement |
|---|
| Proteins quantified | At least 500 proteins |
| Replicates | At least 3 per condition |
| Filtering | 2+ unique peptides per protein |
| Statistical test | limma or t-test with multiple testing correction |
| Pathway enrichment | At least one method (GO, KEGG, or Reactome) |
| Report | Summary, QC, DE results, pathways, visualizations |
Limitations
- Platform-specific : Optimized for MS-based proteomics (not Western blot quantification)
- Missing values : High missing rate (>50% per protein) limits statistical power
- PTM analysis : Requires enrichment protocols for comprehensive PTM profiling
- Absolute quantification : Relative abundance only (unless TMT/SILAC used)
- Protein isoforms : Typically collapsed to gene level
- Dynamic range : MS has limited dynamic range vs mRNA sequencing
References
Methods : MaxQuant (doi:10.1038/nbt.1511), Limma for proteomics (doi:10.1093/nar/gkv007), DEP workflow (doi:10.1038/nprot.2018.107)
Databases : STRING, PhosphoSitePlus, CORUM
Reference Files
- PHASE_DETAILS.md - Detailed procedures for each analysis phase, including report template
Weekly Installs
130
Repository
mims-harvard/to…universe
GitHub Stars
1.2K
First Seen
Feb 19, 2026
Security Audits
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Installed on
codex126
opencode126
gemini-cli125
github-copilot124
cursor122
kimi-cli121
